conkit.core.mappings module

Mappings required for the core functionality

class AminoAcidMapping

Bases: enum.Enum

Amino acid mapping to encode an alignment

A = 1

C = 2

D = 3

E = 4

F = 5

G = 6

H = 7

I = 8

K = 9

L = 10

M = 11

N = 12

P = 13

Q = 14

R = 15

S = 16

T = 17

V = 18

W = 19

X = 21

Y = 20

class AminoAcidOneToThree

Bases: enum.Enum

Amino acid mapping to convert one-letter codes to three-letter codes

A = 'ALA'

B = 'ASX'

C = 'CYS'

D = 'ASP'

E = 'GLU'

F = 'PHE'

G = 'GLY'

H = 'HIS'

I = 'ILE'

J = 'XLE'

K = 'LYS'

L = 'LEU'

M = 'MET'

N = 'ASN'

O = 'PYL'

P = 'PRO'

Q = 'GLN'

R = 'ARG'

S = 'SER'

T = 'THR'

U = 'SEC'

V = 'VAL'

W = 'TRP'

X = 'XAA'

Y = 'TYR'

Z = 'GLX'

class AminoAcidThreeToOne

Bases: enum.Enum

Amino acid mapping to convert three-letter codes to one-letter codes

ALA = 'A'

ARG = 'R'

ASN = 'N'

ASP = 'D'

ASX = 'B'

CME = 'C'

CYS = 'C'

GLN = 'Q'

GLU = 'E'

GLX = 'Z'

GLY = 'G'

HIS = 'H'

ILE = 'I'

LEU = 'L'

LYS = 'K'

MET = 'M'

MSE = 'M'

PHE = 'F'

PRO = 'P'

PYL = 'O'

SEC = 'U'

SER = 'S'

THR = 'T'

TRP = 'W'

TYR = 'Y'

UNK = 'X'

VAL = 'V'

XAA = 'X'

XLE = 'J'

class ContactMatchState

Bases: enum.Enum

Enumerated class to store state constants for each contact

false_negative = 4

false_positive = 3

true_negative = 2

true_positive = 1

unknown = 0

class SequenceAlignmentState

Bases: enum.Enum

Alignment states

aligned = 2

unaligned = 1

unknown = 0